Tomato Functional Genomics Database (TFGD)

Expression of 1-1-6.4.13.20

Experiment: Wild type tomato fruit development (set 1)

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.94956	0.689
27DAP/17DAP	2.72691	0.189
39DAP/27DAP	2.11237	0.215
41DAP/39DAP	0.98868	0.681
42DAP/41DAP	1.44736	0.644
43DAP/42DAP	0.97727	0.914
47DAP/43DAP	0.97829	0.89
52DAP/47DAP	1.1604	0.883
57DAP/52DAP	1.47377	0.758

Experiment: Wild type tomato fruit development (set 2)

hybridization	ratio	FDR (corrected p value)
7DAP/reference	0.88853	0.106
17DAP/reference	1.05445	0.342
27DAP/reference	1.09856	0.115
39DAP/reference	0.99663	0.921
41DAP/reference	1.01955	1
42DAP/reference	0.85116	0.003
43DAP/reference	0.91796	0.039
47DAP/reference	0.97724	0.392
52DAP/reference	1.03904	0.695
57DAP/reference	0.98291	0.553

Experiment: tomato Never-ripe mutant fruit development

hybridization	ratio	FDR (corrected p value)
17DAP/7DAP	0.85587	0.454
27DAP/17DAP	1.04147	0.957
39DAP/27DAP	2.04426	0.062
41DAP/39DAP	2.38534	0.02
42DAP/41DAP	0.84299	0.095
43DAP/42DAP	0.60908	0.022
47DAP/43DAP	1.86704	0.013
52DAP/47DAP	0.66468	0.161
57DAP/52DAP	1.0997	0.902
57DAP/7DAP	1.35775	1

Experiment: tomato rin mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.18628	0.444
17DAP/reference	2.92245	0.006
27DAP/reference	2.281	0.008
39DAP/reference	3.05605	0.006
41DAP/reference	3.32047	0.009
42DAP/reference	3.61737	0.006
43DAP/reference	5.06707	0.006
47DAP/reference	2.19136	0.089
52DAP/reference	3.23579	0.007
57DAP/reference	2.90407	0.004

Experiment: tomato nor mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	1.01482	0.993
17DAP/reference	0.84091	0.023
27DAP/reference	0.80259	0.056
39DAP/reference	0.9267	0.274
41DAP/reference	0.92573	0.169
42DAP/reference	1.05433	1
43DAP/reference	0.87931	0.263
47DAP/reference	0.89653	0.011
52DAP/reference	0.98007	0.5
57DAP/reference	0.94197	0.361

Experiment: tomato hp1 mutant fruit development

hybridization	ratio	FDR (corrected p value)
7DAP/reference	2.41805	0.026
17DAP/reference	1.76932	0.376
27DAP/reference	3.75415	0.029
39DAP/reference	3.46387	0.009
41DAP/reference	2.59026	0.009
42DAP/reference	2.3928	0.041
43DAP/reference	2.53077	0.023
47DAP/reference	1.06196	0.68
52DAP/reference	3.0667	0.061
57DAP/reference	1.786	0.268

Experiment: Wild type pepper fruit development

hybridization	ratio	FDR (corrected p value)
20DAP/14DAP	1.18068	0.966
26DAP/20DAP	2.25514	0.66
34DAP/26DAP	1.04493	1
51DAP/34DAP	0.98544	0.927
52DAP/51DAP	1.02276
53DAP/52DAP	0.92158	0.703
55DAP/53DAP	1.13012	0.922
57DAP/55DAP	1.03991	0.881
62DAP/57DAP	0.91788	0.871
68DAP/62DAP	1.42223	0.36
68DAP/14DAP	1.24908	0.161

Experiment: Tomato (breaker-stage) vs. Pepper (breaker-stage)

hybridization	ratio	FDR (corrected p value)
Tomato Breaker/Pepper Breaker	4.06281	0.014

Experiment: Solanaceae fruit comparison

hybridization	ratio	FDR (corrected p value)
Green Pepper/Ripe Pepper	0.00291
Mature Green Tomato/Ripe Tomato	N/A	N/A
Immature Eggplant/Mature Eggplant	1.02756
Ripe Pepper/Ripe Tomato	0.12098	0.224
Mature Eggplant/Ripe Tomato	0.10835	0.234

Experiment: IL carotenoid

hybridization	ratio	FDR (corrected p value)
11-1/M82	1.03098	1
1-1-2/M82	1.53181	1
12-2/M82	1.37112	1
12-4/M82	0.27796	0.619
1-3/M82	0.9957	1
2-1-1/M82	3.22569	0.375
2-1/M82	6.77564	0.32
2-6/M82	0.60054	0.501
3-2/M82	0.59224	1
4-1-1/M82	0.69961	1
4-1/M82	N/A	N/A
4-3-2/M82	0.44794	0.37
4-3/M82	0.75747	0.72
5-3/M82	1.61113	1
6-2/M82	0.57012
6-3/M82	0.84654	1
7-1/M82	0.68877	0.803
7-2/M82	0.85238	0.881
9-3-2/M82	0.54848	0.355

Experiment: Tomato introgression line transcript analysis

hybridization	ratio	FDR (corrected p value)
IL4-4/WTpooled	1.19693
IL2-6/WTpooled	0.84724	1
IL7-5/WTpooled	0.4651
IL7-3/WTpooled	0.99093	1
IL12-4/WTpooled	1.35256	0.503
IL1-4/WTpooled	0.82554	0.476
WT/WTpooled	1.02021	1

Experiment: Transcriptional changes determined by expression of the Xanthomonas AvrRxv effector in resistant tomato plants

hybridization	ratio	FDR (corrected p value)
10 h post inoculation	1.45601	0.193

Experiment: Time course of DC3000 vs delta hrp on tomato Prf-3

hybridization	ratio	FDR (corrected p value)
DC3000/delat hrp 0h	1.07157	0.921
DC3000/delta hrp 6h	2.32389	1
DC3000/delta hrp 12h	0.74289	1
DC3000/delta hrp 24h	0.95035	0.692

Experiment: DC3000 effector mutants

hybridization	ratio	FDR (corrected p value)
DC3000 delta A/DC3000 delta AB	N/A	N/A
DC3000 delta B/DC3000 delta AB	N/A	N/A

Experiment: Matt's wild cherry tomato vs. Phytophthora infestans

hybridization	ratio	FDR (corrected p value)
Exp 12h	0.76029	1
Exp 36h	N/A	N/A
Exp 60h	2.63117	0.283

Experiment: Gene expression profiling of infection of tomato by Phytophthora infestans in the field

hybridization	ratio	FDR (corrected p value)
self-self	N/A	N/A
Var 0h	0.8877	0.244
Var 12h I row2-row1	N/A	N/A
Var 12h NI row2-row1	N/A	N/A
Var 36h I row2-row1	N/A	N/A
Var 36h NI row2-row1	N/A	N/A
Var 60h I row2-row1	2.2959	0.562
Var 60h NI row2-row1	1.57888
Time course 0hI-0hNI	N/A	N/A
Time course 12hI-12hNI	N/A	N/A
Time course 36hI-36hNI	5.75584	0.005
Time course 60hI-60hNI	N/A	N/A

Experiment: Transcriptional profiling of the tomato fruit pericarp tissue: fruits overexpressing yeast ySAMdc gene and controls

hybridization	ratio	FDR (corrected p value)
transgenic ySAMdc/azygous control (mature green)	1.1037	0.748
transgenic ySAMdc/azygous control (breaker)	0.84451	0.49
transgenic ySAMdc/azygous control (red)	1.2853	1

Experiment: Tomato root culture and Al treatment

hybridization	ratio	FDR (corrected p value)
Al-treated/control	1.02395	0.471

Experiment: Microarray Analysis on Salt Stress Affected Genes in Tomato Seedlings

hybridization	ratio	FDR (corrected p value)
salt-treated/no salt	0.53484	0.238

Experiment: Transcriptional Profiling of high pigment-2dg Tomato Mutant Fruit

hybridization	ratio	FDR (corrected p value)
Manapal/WT (mature green)	1.08075	1
Manapal/WT (break)	2.4787	0.183
Manapal/WT (red)	1.20648	0.164